MolNFT v1 · #74500 · protein + DNA
Crystal structure of the pfv S217H mutant intasome bound to manganese
3OYK · Pfv integrase: “Crystal structure of the pfv S217H mutant intasome bound to manganese”. X-ray diffraction, 4 ligands (MN, ZN, SO4), 8 pockets (best druggability 0.71). MolNFT v1 #74500 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3OYK
- Type
- protein + DNA
- Length
- 584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pfv integrase; DNA (5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')…
- UniProt
- P14350
- Ligands
- MN, ZN, SO4, NH4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfv integrase | protein | 368 | 34% helix, 21% strand | P14350 |
| B | Pfv integrase | protein | 180 | 39% helix, 17% strand | P14350 |
| C | DNA (5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3') | dna | 19 | — | — |
| D | DNA (5'- D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3') | dna | 17 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, D, B
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.71 | 0.81 | 67 | empty |
| 2 | 544 | 0.69 | 0.78 | 43 | empty |
| 3 | 225 | 0.53 | 0.77 | 27 | SO4 |
| 4 | 70 | 0.50 | 0.85 | 16 | empty |
| 5 | 83 | 0.32 | 0.74 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1432 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1128 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 746 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–D · 357 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 3OYK · Crystal structure of the PFV S217H mutant intasome bound to manganese · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P14350
- Elsewhere: RCSB PDB 3OYK · PDBe 3OYK · UniProt P14350
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